miRdSNP: A database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Bruno, Andrew E ^a   Li, Li ^b   Kalabus, James L ^a   Pan, Yuzhuo ^a   Yu, Aiming ^a   Hu, Zihua ^a,c,d  

^a UNIVERSITY AT BUFFALO   (United States)

^b Beijing Jishuitan Hospital   (China)

^c Department of Medicine ^*  (United States)

^d SUNY EYE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

3' UNTRANSLATED REGION; ALGORITHM; ARTICLE; BRAIN COMPUTER INTERFACE; GENE LINKAGE DISEQUILIBRIUM; GENE TARGETING; GENERAL ASPECTS OF DISEASE; GENETIC VARIABILITY; HUMAN; PREDICTION; SINGLE NUCLEOTIDE POLYMORPHISM; WEB BROWSER; COMPUTER PROGRAM; DISEASES; GENETIC DATABASE; GENETICS; INTERNET; METABOLISM;

3' UNTRANSLATED REGIONS; ALGORITHMS; DATABASES, GENETIC; DISEASE; HUMANS; INTERNET; MICRORNAS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84856105903     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-44     Document Type: Article

References (31)

1. Dickson DW, Baker M, Rademakers R. Common variant in GRN is a genetic risk factor for hippocampal sclerosis in the elderly. Neurodegener Dis 2010, 7(1-3):170-174. 10.1159/000289231, 2859236, 20197700.
2. Wang G, van der Walt JM, Mayhew G, Li YJ, Züchner S, Scott WK, Martin ER, Vance JM. Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein. Am J Hum Genet 2008, 82(2):283-289. 10.1016/j.ajhg.2007.09.021, 2427225, 18252210.
3. Abelson JF, Kwan KY, O'Roak BJ, Baek DY, Stillman AA, Morgan TM, Mathews CA, Pauls DL, Rasin MR, Gunel M, Davis NR, Ercan-Sencicek AG, Guez DH, Spertus JA, Leckman JF, Dure LS, Kurlan R, Singer HS, Gilbert DL, Farhi A, Louvi A, Lifton RP, Sestan N, State MW. Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science 2005, 310(5746):317-320. 10.1126/science.1116502, 16224024.
4. Tan Z, Randall G, Fan J, Camoretti-Mercado B, Brockman-Schneider R, Pan L, Solway J, Gern JE, Lemanske RF, Nicolae D, Ober C. Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am J Hum Genet 2007, 81(4):829-834. 10.1086/521200, 2227932, 17847008.
5. Martin MM, Buckenberger JA, Jiang J, Malana GE, Nuovo GJ, Chotani M, Feldman DS, Schmittgen TD, Elton TS. The human angiotensin II type 1 receptor +1166 A/C polymorphism attenuates microrna-155 binding. J Biol Chem 2007, 282(33):24262-24269. 10.1074/jbc.M701050200, 2413065, 17588946.
6. Rademakers R, Eriksen JL, Baker M, Robinson T, Ahmed Z, Lincoln SJ, Finch N, Rutherford NJ, Crook RJ, Josephs KA, Boeve BF, Knopman DS, Petersen RC, Parisi JE, Caselli RJ, Wszolek ZK, Uitti RJ, Feldman H, Hutton ML, Mackenzie IR, Graff-Radford NR, Dickson DW. Common variation in the miR-659 binding-site of GRN is a major risk factor for TDP43-positive frontotemporal dementia. Hum Mol Genet 2008, 17(23):3631-3642. 10.1093/hmg/ddn257, 2581433, 18723524.
7. Schaefer AS, Richter GM, Nothnagel M, Laine ML, Rühling A, Schäfer C, Cordes N, Noack B, Folwaczny M, Glas J, Dörfer C, Dommisch H, Groessner-Schreiber B, Jepsen S, Loos BG, Schreiber S. A 3' UTR transition within DEFB1 is associated with chronic and aggressive periodontitis. Genes Immun 2010, 11:45-54. 10.1038/gene.2009.75, 19829306.
8. Nicoloso MS, Sun H, Spizzo R, Kim H, Wickramasinghe P, Shimizu M, Wojcik SE, Ferdin J, Kunej T, Xiao L, Manoukian S, Secreto G, Ravagnani F, Wang X, Radice P, Croce CM, Davuluri RV, Calin GA. Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Cancer Res 2010, 70(7):2789-2798. 10.1158/0008-5472.CAN-09-3541, 2853025, 20332227.
9. Brendle A, Lei H, Brandt A, Johansson R, Enquist K, Henriksson R, Hemminki K, Lenner P, Försti A. Polymorphisms in predicted microRNA-binding sites in integrin genes and breast cancer: ITGB4 as prognostic marker. Carcinogenesis 2008, 29(7):1394-1399. 10.1093/carcin/bgn126, 18550570.
10. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I, Muller RU, Straka E, Su L, Burki EA, Crowell RE, Patel R, Kulkarni T, Homer R, Zelterman D, Kidd KK, Zhu Y, Christiani DC, Belinsky SA, Slack FJ, Weidhaas JB. A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk. Cancer Res 2008, 68(20):8535-8540. 10.1158/0008-5472.CAN-08-2129, 2672193, 18922928.
11. He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, Volinia S, Calin GA, Liu CG, Franssila K, Suster S, Kloos RT, Croce CM, de la Chapelle A. The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci USA 2005, 102(52):19075-19080. 10.1073/pnas.0509603102, 1323209, 16365291.
12. Saetrom P, Biesinger J, Li SM, Smith D, Thomas LF, Majzoub K, Rivas GE, Alluin J, Rossi JJ, Krontiris TG, Weitzel J, Daly MB, Benson AB, Kirkwood JM, O'Dwyer PJ, Sutphen R, Stewart JA, Johnson D, Larson GP. A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis. Cancer Res 2009, 69(18):7459-7465. 10.1158/0008-5472.CAN-09-1201, 2747041, 19738052.
13. Mishra PJ, Humeniuk R, Mishra PJ, Longo-Sorbello GSA, Banerjee D, Bertino JR. A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci USA 2007, 104(33):13513-13518. 10.1073/pnas.0706217104, 1948927, 17686970.
14. Hu Z, Bruno AE. The Influence of 3'UTRs on microRNA Function Inferred from Human SNP Data. Comparative and Functional Genomics 2011, 2011., http://dx.doi.org/10.1155/2011/910769
15. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res 2007, 35(Database):D51-D54. 10.1093/nar/gkl797, 1669716, 17099235.
16. Hiard S, Charlier C, Coppieters W, Georges M, Baurain D. Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res 2010, 38(Database):D640-D651. 10.1093/nar/gkp926, 2808989, 19906729.
17. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20. 10.1016/j.cell.2004.12.035, 15652477.
18. Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions. Nat Genet 2005, 37(5):495-500. 10.1038/ng1536, 15806104.
19. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. 186604, 12045153.
20. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29:308-311. 10.1093/nar/29.1.308, 29783, 11125122.
21. Consortium IH, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MMY, Tsui SKW, Xue H, Wong JTF, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PKH, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PIW, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe''er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CDM, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449(7164):851-861. 10.1038/nature06258, 2689609, 17943122.
22. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, de Bakker PIW. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 2008, 24(24):2938-2939. 10.1093/bioinformatics/btn564, 2720775, 18974171.
23. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 2009, 25(23):3049-3055. 10.1093/bioinformatics/btp565, 19789267.
24. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, 34(Database):D140-D144. 1347474, 16381832.
25. Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 2006, 12(2):192-197. 1370898, 16373484.
26. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2011, 39(Database):D163-D169. 10.1093/nar/gkq1107, 3013699, 21071411.
27. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, 37(Database):D105-D110. 10.1093/nar/gkn851, 2686554, 18996891.
28. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 2009, 37(Database):D98-104. 10.1093/nar/gkn714, 2686559, 18927107.
29. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol 2003, 5:R1. 10.1186/gb-2003-5-1-r1, 395733, 14709173.
30. Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG. Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 2009, 10:295. 10.1186/1471-2105-10-295, 2752464, 19765283.
31. Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 2007, 8:69. 10.1186/1471-2105-8-69, 1838429, 17331257.